Hundreds of principals are having "ongoing problems" with a new payroll system, a survey suggests.

The Education Ministry last month switched to the Australian-owned Novopay system for paying teachers. Last week marked the fourth round of pay under the new system.

Some teachers and principals have reported continuing problems with the new system, with some being massively under-paid and unexplained sick leave showing up for others.

In a survey conducted by the New Zealand Principals' Federation (NZPF), 90 per cent of principals that responded said they had "on-going problems yet to be resolved from previous pay rounds". Some 86 per cent had no confidence their problems would be resolved by the end of the year.

A little under half of the principals from 2400 schools contacted nationwide responded to the NZPF survey.

About 200 principals in the survey reported not having all their staff paid correctly in the latest pay round, NZPF president Paul Drummond said.

"This is the fourth pay roll since Novopay was introduced. What we have now are not teething problems," Drummond said.

"They are clearly systemic."

Education Ministry chief information officer, Leanne Gibson, has said Novopay was improving, with only 60 staff not paid or underpaid in the latest pay round. This was down from more than 1000 in a previous cycle and less than under the old system, which usually failed to correctly pay between 100 and 150 staff each pay day.

"The ministry is working hard to address any issues where they arise and no staff member will be left financially disadvantaged," she said.